In recent years, mass spectrometers capable of performing MSn analysis are widely used for structure analysis of various substances including polymer compounds. Specifically, when an ion originating from a component of interest contained in a sample is dissociated by collision induced dissociation (CID), a molecular bond is broken at a specific site depending on the bond energy or other factors, so that various product ions and neutral losses are produced. Therefore, an ion having a specific mass-to-charge ratio m/z corresponding to a component of interest is selected from various ions produced from a sample, the selected ion is dissociated by CID, and various product ions produced by the dissociation are subjected to mass analysis to obtain an MS2 spectrum. Since the MS2 spectrum includes information about various fragments (including product ions and neutral losses) originating from the component of interest, the chemical structure of the component of interest can be estimated by analyzing the MS2 spectrum data.
Actually, however, it is not always easy to determine a structural formula of an unidentified substance by utilizing information collected from an MS2 spectrum obtained by a single dissociation operation or from an MSn spectrum obtained through a plurality of repeated dissociation operations. A polymer compound composed of specific elements and having a one-dimensional (linear) sequence structure, such as amino acids, can be comparatively easily assessed (or estimated) for its structure from an MSn spectrum. On the contrary, general low molecular weight compounds having a molecular weight of about 50 to 1000 have a variety of structural formulas and are complicated in the sequence, and therefore, it is difficult in many cases to estimate their structures from an MSn spectrum. A structural analysis method useful in such a case is database search using a database storing MSn peak patterns and the like of known substances (see Patent Document 1, for example). Since the number of known substances stored in a database is, however, limited, the search often results in no hits.
In synthesis of, for example, a pharmaceutical, not only a substance of interest but also a large number of byproducts having similar structures are simultaneously produced, and hence, it is sometimes desired to study structural similarity and difference among various byproducts contained in a sample. Alternatively, in studying metabolism of a pharmaceutical in vivo, it may be desired to find structural similarity and difference among a large number of metabolites including an unidentified substance. In these cases, although information about a substance of interest having a known structure may be stored in a database, the database cannot generally store information about all byproducts and metabolites having slightly different structures. Therefore, there often remains an unidentified substance whose structural formula cannot be determined even if the database is searched.